collectcommand.cpp

   1 /*
   2  *  collectcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "collectcommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "npshannon.h"
  18 #include "shannon.h"
  19 #include "jackknife.h"
  20
  21
  22 //**********************************************************************************************************************
  23
  24
  25 CollectCommand::CollectCommand(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 string fileNameRoot;
  29                 fileNameRoot = getRootName(globaldata->inputFileName);
  30                 int i;
  31                 validCalculator = new ValidCalculators();
  32
  33                 for (i=0; i<globaldata->Estimators.size(); i++) {
  34                         if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
  35                                 if (globaldata->Estimators[i] == "sobs") {
  36                                         cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
  37                                 }else if (globaldata->Estimators[i] == "chao") {
  38                                         cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
  39                                 }else if (globaldata->Estimators[i] == "nseqs") {
  40                                         cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
  41                                 }else if (globaldata->Estimators[i] == "ace") {
  42                                         convert(globaldata->getAbund(), abund);
  43                                         cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
  44                                 }else if (globaldata->Estimators[i] == "jack") {
  45                                         cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
  46                                 }else if (globaldata->Estimators[i] == "shannon") {
  47                                         cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
  48                                 }else if (globaldata->Estimators[i] == "npshannon") {
  49                                         cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
  50                                 }else if (globaldata->Estimators[i] == "simpson") {
  51                                         cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
  52                                 }else if (globaldata->Estimators[i] == "bootstrap") {
  53                                         cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
  54                                 }
  55                         }
  56                 }
  57
  58                 //reset calc for next command
  59                 globaldata->setCalc("");
  60         }
  61         catch(exception& e) {
  62                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65         catch(...) {
  66                 cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  67                 exit(1);
  68         }
  69
  70 }
  71
  72 //**********************************************************************************************************************
  73
  74 CollectCommand::~CollectCommand(){
  75         delete order;
  76         delete input;
  77         delete cCurve;
  78         delete read;
  79 }
  80
  81 //**********************************************************************************************************************
  82
  83 int CollectCommand::execute(){
  84         try {
  85                 int count = 1;
  86
  87                 //if the users entered no valid calculators don't execute command
  88                 if (cDisplays.size() == 0) { return 0; }
  89
  90                 read = new ReadPhilFile(globaldata->inputFileName);
  91                 read->read(&*globaldata);
  92
  93                 order = globaldata->gorder;
  94                 input = globaldata->ginput;
  95                 set<string> orderList;
  96
  97                 while(order != NULL){
  98
  99                         orderList.insert(order->getLabel());
 100                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 101                                 cCurve = new Collect(order, cDisplays);
 102                                 convert(globaldata->getFreq(), freq);
 103                                 cCurve->getCurve(freq);
 104
 105                                 delete cCurve;
 106
 107                                 cout << order->getLabel() << '\t' << count << endl;
 108                         }
 109                         order = (input->getOrderVector());
 110                         count++;
 111                 }
 112                 set<string>::iterator i;
 113                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 114                         if(orderList.count(*i) == 0)
 115                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 116                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 117                 return 0;
 118         }
 119         catch(exception& e) {
 120                 cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 121                 exit(1);
 122         }
 123         catch(...) {
 124                 cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 125                 exit(1);
 126         }
 127 }
 128
 129 //**********************************************************************************************************************